› 5wt9

X-ray diffraction
2.4Å resolution

Complex structure of PD-1 and nivolumab-Fab

Released:
DOI: 10.2210/pdb5wt9/pdb
PDB entry 5wt9 coloured by chain, front view.
PDB entry 5wt9 coloured by chain, side view.
PDB entry 5wt9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
An unexpected N-terminal loop in PD-1 dominates binding by nivolumab.
Tan S, Zhang H, Chai Y, Song H, Tong Z, Wang Q, Qi J, Wong G, Zhu X, Liu WJ, Gao S, Wang Z, Shi Y, Yang F, Gao GF, Yan J
Nat Commun 8 14369 (2017)
PMID: 28165004

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-235380 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Heavy Chain of Nivolumab Chain: H
Molecule details ›
Chain: H
Length: 220 amino acids
Theoretical weight: 23.68 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Light Chain of Nivolumab Chain: L
Molecule details ›
Chain: L
Length: 217 amino acids
Theoretical weight: 23.64 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Programmed cell death protein 1 Chain: G
Molecule details ›
Chain: G
Length: 173 amino acids
Theoretical weight: 19.65 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q15116 (Residues: 1-167; Coverage: 54%)
Gene names: PD1, PDCD1
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P43212
Unit cell:
a: 108.527Å b: 108.527Å c: 145.423Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.187 0.228
Expression system: Homo sapiens

Quick links

Citations

28 review citations

Immune checkpoint signaling and cancer immunotherapy.
He et al. (2020)
27 more

33 mentions without citation

A molecular and preclinical comparison of the PD-1-targeted T-cell checkpoint inhibitors nivolumab and pembrolizumab.
Fessas et al. (2017)
32 more